= The BIOS Consortium (Biobank-based Integrative Omics Studies) = '''Welcome to the Wiki of the BIOS Consortium.''' The mission of the BIOS Consortium is to create a large-scale data infrastructure and to bring together BBMRI researchers focusing on integrative omics studies in Dutch Biobanks. The advent of the genome-wide association study (GWAS) led to the successful identification of thousands of variants that are robustly associated with complex disease phenotypes. Dutch biobanks played a substantial role in these discoveries. For most of these variants, however, the mechanisms through which they contribute to these phenotypes remain unknown. The BIOS Consortium applies a functional genomics approach that integrates genome-wide genetic data with data on the epigenome and transcriptome to elucidate these mechanisms. Over 4000 samples from BBMRI-NL biobanks with in-depth information on disease phenotypes and GWAS data are being enriched with RNA-sequencing and genome-wide DNA methylation data. The same is true for samples with whole-genome sequencing data from GoNL. This unique data infrastructure provides a powerful platform to evaluate key questions in integrative omics from establishing comprehensive eQTL and meQTL catalogues to linking molecular pathways across omics levels to phenotypic outcomes. See also [https://www.bbmri.nl/on_offer/bios/ our BBMRI website] '''Note:''' Read [wiki:FgWiki Using this wiki] before making changes to these pages. = Table of contents = * '''BIOS data accessibility and locations''' * [wiki:BIOS_bios Getting access to BIOS data] - Instructions on how to request access to the BIOS datasets. * [wiki:BIOS_VirtualMachine Accessing the BIOS Virtual Machine and Grid SRM] - Description of the various methods to connect to BIOS resources. * [wiki:BIOS_PreparedData Recommended BIOS datasets for downstream analysis] - One page overview of all BIOS datasets available on the BIOS VM. * [wiki:BIOS_Metadatabase Metadatabase] - Description of the metadatabase where all BIOS metadata are stored. * [wiki:BIOS_DataInfrastructure Grid data infrastructure] - Descriptions and locations regarding data storage on Grid. * [http://bios-vm.bbmrirp3-lumc.vm.surfsara.nl/BIOSRutils/ BIOSRutils] - Accessing and analyzing BIOS data from within a R package. * '''Infrastructure and data on Groningen Cluster''' * [wiki:BIOS_UMCGFileStructure UMCG file structure] - Descriptions and locations regarding computation resources and project datasets on the Groningen Cluster. * '''Main BIOS Papers''' * First eQTL paper - 'Hypothesis-free identification of modulators of genetic risk factors' (in revision at Nature Genetics http://biorxiv.org/content/early/2015/11/30/033217), see attached file for RNA-seq QC and processing. * First meQTL paper - 'Disease variants alter transcription factor levels and methylation of their binding sites' (in revision at Nature Genetics, http://biorxiv.org/content/early/2015/12/01/033084.1). See also [https://git.lumc.nl/molepi/Leiden450K Methylation QC and processing]. * '''Organisation''' * [wiki:BIOS_team The BIOS team] * [wiki:BIOS_Wiki Using this wiki] - Notes on editing and structuring our wiki pages. * '''[wiki:FgPrivate Private] '''